PDB-4zor: The structure of the S37P MS2 viral capsid assembly.

ID or keywords:

Entry

Database: PDB / ID: 4zor

Title

The structure of the S37P MS2 viral capsid assembly.

Components

Coat protein

Keywords

VIRUS /

Capsid /

VIRUS LIKE PARTICLE

Function / homology

Function and homology information

negative regulation of viral translation / T=3 icosahedral viral capsid /

regulation of translation / structural molecule activity /

RNA binding / identical protein binding
Similarity search - Function

Biological species

Enterobacteria phage MS2 (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Asensio, M.A. / Sankaran, B. / Zwart, P.H. / Tullman-Ercek, D.

Citation

Journal: Nano Lett. / Year: 2016
Title: A Selection for Assembly Reveals That a Single Amino Acid Mutant of the Bacteriophage MS2 Coat Protein Forms a Smaller Virus-like Particle.
Authors: Asensio, M.A. / Morella, N.M. / Jakobson, C.M. / Hartman, E.C. / Glasgow, J.E. / Sankaran, B. / Zwart, P.H. / Tullman-Ercek, D.

History

Deposition	May 6, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 7, 2016	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2016	Group: Database references
Revision 1.2	Sep 27, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4zor.cif.gz	357 KB	Display	PDBx/mmCIF format
PDB format	pdb4zor.ent.gz	302.9 KB	Display	PDB format
PDBx/mmJSON format	4zor.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zo/4zor ftp://data.pdbj.org/pub/pdb/validation_reports/zo/4zor	HTTPS FTP

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Related structure data

Related structure data	2ms2S S: Starting model for refinement
Similar structure data	6yfr-d 1558 1552 5cw0-1 1a34-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#200 - Aug 2016 Quasisymmetry in Icosahedral Viruses similarity (1)

Deposited unit

A: Coat protein

B: Coat protein

C: Coat protein

D: Coat protein

E: Coat protein

hetero molecules

69.1 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Coat protein

B: Coat protein

C: Coat protein

D: Coat protein

E: Coat protein

hetero molecules

x 12

defined by author&software
829 kDa, 60 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Type	Name	Symmetry operation	Number
identity operation	1_555	x,y,z	1
crystal symmetry operation	2_665	-x+1,-y+1,z	1
crystal symmetry operation	3_656	-x+1,y,-z+1	1
crystal symmetry operation	4_566	x,-y+1,-z+1	1
crystal symmetry operation	5_555	z,x,y	1
crystal symmetry operation	6_566	z,-x+1,-y+1	1
crystal symmetry operation	7_665	-z+1,-x+1,y	1
crystal symmetry operation	8_656	-z+1,x,-y+1	1
crystal symmetry operation	9_555	y,z,x	1
crystal symmetry operation	10_656	-y+1,z,-x+1	1
crystal symmetry operation	11_566	y,-z+1,-x+1	1
crystal symmetry operation	12_665	-y+1,-z+1,x	1

Unit cell

Length a, b, c (Å)	228.125, 228.125, 228.125
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	196
Space group name H-M	F23

Components on special symmetry positions

ID	Model	Components
1	1	A-201- PO4
2	1	A-201- PO4
3	1	D-201- PO4
4	1	D-201- PO4
5	1	A-306- HOH
6	1	A-323- HOH
7	1	C-255- HOH

#1: Protein	Coat protein Mass: 13748.501 Da / Num. of mol.: 5 / Mutation: S38P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Enterobacteria phage MS2 (virus) / Production host: Escherichia coli K-12 (bacteria) / References: UniProt: P03612
#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO₄
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 432 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION

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Sample preparation

Crystal	Density Matthews: 3.6 Å³/Da / Density % sol: 65.81 %
Crystal grow	Temperature: 299 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 1.8M lithium sulphate, 100mM TRIS, pH 7.55, 20% glycerol (cryo)

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 29, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 2.2→43.9 Å / Num. obs: 49435 / % possible obs: 99.9 % / Redundancy: 5 % / B_iso Wilson estimate: 34.36 Å² / R_merge(I) obs: 0.1448 / Net I/σ(I): 7.7
Reflection shell	Resolution: 2.2→2.281 Å / Redundancy: 4.8 % / R_merge(I) obs: 1.577 / Mean I/σ(I) obs: 1.02 / Num. unique all: 4867 / % possible all: 0.99

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Processing

Software

Name	Version	Classification
PHENIX	DEV_1839	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 2MS2

2ms2

Resolution: 2.2→43.9 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 27.48 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2425	1994	4.06 %
R_work	0.2177	-	-
obs	0.219	49102	98.9 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.2→43.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4731	0	20	432	5183

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	4870
X-RAY DIFFRACTION	f_angle_d	0.989	6619
X-RAY DIFFRACTION	f_dihedral_angle_d	11.995	1742
X-RAY DIFFRACTION	f_chiral_restr	0.038	775
X-RAY DIFFRACTION	f_plane_restr	0.004	860

LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection obs	% reflection obs (%)
2.2021-2.2571	0.4348	189	0.3868	3117	4596	92
2.2571-2.3182	0.3647	139	0.319	3275		98
2.3182-2.3864	0.3041	147	0.2716	3390		99
2.3864-2.4634	0.2639	140	0.2652	3344		99
2.4634-2.5514	0.3123	139	0.2605	3368		100
2.5514-2.6536	0.2674	146	0.2737	3386		100
2.6536-2.7743	0.3172	148	0.2648	3360		100
2.7743-2.9206	0.2889	145	0.2548	3377		100
2.9206-3.1035	0.2483	143	0.2274	3385		100
3.1035-3.343	0.2463	144	0.2119	3395		100
3.343-3.6793	0.2004	144	0.1975	3394		99
3.6793-4.2114	0.1919	138	0.1841	3381		99
4.2114-5.3044	0.1931	142	0.1595	3421		100
5.3044-43.9114	0.2241	147	0.2017	3513		100

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	0.1075	-0.1697	-0.3831	1.5681	-0.5052	1.4364	-0.0708	0.0249	0.0524	-0.0885	0.0413	-0.4125	-0.392	0.0869	-0.0002	0.4373	-0.0416	-0.0217	0.4266	-0.006	0.4746	142.1107	162.3261	64.3308
2	0.5326	0.1975	-0.1561	0.1485	0.1804	0.4904	-0.103	-0.2199	-0.2295	0.2061	0.2341	-0.122	0.5123	0.1608	0.001	0.6065	0.0508	-0.0299	0.5092	0.0282	0.5359	144.2816	143.8084	67.6934
3	1.203	1.0397	-0.0681	1.1387	-0.2305	1.4658	-0.0818	-0.1608	-0.015	-0.1025	0.2321	0.1874	-0.2018	0.0119	0.0003	0.4317	-0.0191	-0.0796	0.467	-0.001	0.3701	134.5308	157.0436	67.2032
4	1.3627	-0.9341	-0.3343	0.3476	0.3692	1.1796	-0.1251	-0.248	-0.0854	-0.0935	0.2251	0.1143	-0.1781	0.0813	0.0014	0.4088	-0.033	0.0069	0.4551	0.0139	0.4506	134.98	154.1344	66.078
5	0.1544	0.0552	0.1006	0.392	0.2254	0.449	-0.1702	0.1969	-0.1693	-0.244	0.2667	-0.1069	-0.4171	0.3374	0.0002	0.3995	-0.0091	0.0405	0.4711	-0.0101	0.4519	143.2988	144.5427	51.1223
6	0.5484	-0.7156	0.3686	0.9676	-0.2823	0.5106	0.0048	0.2096	-0.3087	-0.5451	-0.2416	0.5486	-0.2413	0.0496	-0.0001	0.479	0.0208	-0.0567	0.4673	-0.0087	0.5149	124.505	150.5081	50.0012
7	3.3916	-0.7351	0.032	2.0601	0.8903	1.4356	0.2228	-0.0532	0.6556	0.1179	0.166	0.0303	-0.5491	-0.1369	0.0005	0.48	0.021	0.0152	0.4178	-0.0267	0.5094	140.2699	182.5214	99.1292
8	0.2353	-0.1471	0.0019	0.1607	-0.0329	-0.0011	-0.1878	0.1294	0.1689	-0.2714	0.1617	0.3499	-0.4527	-0.2132	-0.0007	0.488	0.0648	0.0227	0.5117	0.01	0.4197	130.0875	181.3225	93.2368
9	1.4104	-0.0177	-0.764	1.1293	0.5566	0.9186	-0.0649	-0.2325	-0.0395	0.2271	-0.063	-0.2564	0.223	-0.1938	0.0007	0.4964	-0.0313	0.0237	0.4736	-0.0016	0.3988	144.7876	168.097	102.908
10	1.7254	-0.532	0.4113	0.29	0.1162	2.0065	0.0914	0.2252	0.1055	-0.0511	-0.0686	0.0234	-0.0588	0.0464	-0	0.4646	-0.0089	0.0289	0.3635	0.0278	0.425	147.6598	171.6044	90.6153
11	2.209	0.0912	1.3393	1.9666	0.8169	2.6384	-0.0977	0.0525	0.3396	-0.0469	0.1386	0.1605	-0.4525	-0.3832	-0.0001	0.4869	-0.0006	0.0023	0.4884	0.0177	0.4466	100.7431	186.0533	104.4885
12	0.8388	-0.0162	0.0471	0.3738	0.3593	0.2403	0.0711	-0.0706	-0.2629	0.1504	-0.0839	0.1622	1.249	-0.0685	0.0024	0.6781	-0.046	0.0421	0.5327	0.0206	0.5129	103.8294	174.7087	119.3646
13	2.3228	-0.3355	0.2295	3.1755	0.2474	0.239	-0.3785	0.5581	-0.1602	-0.198	-0.2263	0.0071	0.5104	-0.73	0.0008	0.3807	-0.0669	0.0334	0.5338	-0.0468	0.4335	107.9631	178.9862	105.3338
14	0.6379	0.1667	-0.7726	0.284	-0.0747	0.7098	-0.0779	0.083	-0.0432	-0.0861	-0.0654	0.0404	0.0316	-0.0171	-0.0014	0.4579	0.0018	0.0171	0.4598	0.0021	0.4713	110.0525	178.6155	112.0088
15	0.1732	0.1598	0.1599	0.3847	-0.0171	0.3041	0.0793	-0.0005	0.3626	0.0517	-0.1245	0.0648	-0.3404	0.1471	0.0011	0.4896	0.0049	-0.0048	0.4349	-0.0092	0.4383	112.127	188.696	123.3839
16	0.6239	0.1817	0.3139	0.3496	-0.2992	0.7631	0.0429	-0.2054	0.1653	-0.0582	0.0191	-0.0213	0.0901	0.8114	0.0007	0.5081	-0.0494	0.0228	0.6214	0.0227	0.4351	126.0236	187.2638	109.4036
17	2.5323	-0.5673	-0.3605	1.1041	0.3626	2.4472	-0.0074	0.4099	0.1146	-0.7865	-0.038	0.2514	-0.3622	-0.3544	0.0001	0.5006	-0.0044	-0.0272	0.5481	0.0564	0.4094	79.4026	168.1745	77.0078
18	0.192	-0.0862	-0.0025	0.038	-0.0253	0.109	-0.127	0.2125	0.1327	-0.0593	0.1	-0.0408	0.0931	0.1761	-0.0001	0.5206	-0.0205	0.0285	0.4852	-0.0018	0.4213	90.8914	169.0301	74.5392
19	0.338	-0.4342	-0.0766	0.6573	0.1787	0.4181	-0.1812	-0.3516	-0.6149	-0.0505	-0.2937	-0.0983	0.2954	0.5748	-0.0011	0.5019	0.0241	0.0273	0.4747	0.0527	0.628	76.5254	156.0857	89.9596
20	1.0769	-1.388	0.5487	2.3172	-0.0784	1.4306	0.1806	0.0517	-0.6209	-0.0694	-0.4287	-0.6602	-0.3554	0.2131	-0.0037	0.5071	-0.0276	0.0045	0.4399	-0.0332	0.4282	88.5292	166.2284	83.9076
21	0.383	-0.1248	0.2247	0.4166	-0.2643	0.128	-0.0054	0.0341	-0.0965	-0.0097	-0.0989	-0.0619	-0.1203	0.0478	-0.0002	0.5059	0.0032	-0.0026	0.4445	-0.0061	0.4273	83.4783	164.815	89.3589
22	0.7944	-0.4301	-0.4594	0.8007	-0.1793	0.8109	0.1299	-0.1553	0.3354	-0.0667	-0.1524	0.0785	-0.2811	0.1099	-0.0001	0.5317	-0.01	0.0349	0.4549	0.0068	0.3941	77.1576	175.5344	96.6432
23	1.2929	0.3183	0.2434	0.3476	-0.2987	0.5471	0.2179	1.304	-0.2729	-0.7913	-0.2702	-0.0501	0.5358	-0.2418	-0.0036	0.6223	-0.0575	0.0045	0.7094	0.0352	0.4741	104.979	150.2365	47.1329
24	2.3383	0.9317	-1.3881	1.5526	0.5878	1.9688	0.1114	0.4287	0.2267	-0.1916	0.0236	-0.4048	-0.1418	-0.2548	-0.0002	0.4145	0.0086	0.0085	0.518	-0.0028	0.4832	108.341	154.6405	53.8058
25	0.3004	-0.2483	0.2213	0.3022	-0.1297	0.7531	0.3246	-0.3829	-0.5598	0.7918	-0.3749	-0.1888	0.0506	0.0954	-0.0025	0.5963	0.033	-0.0768	0.5648	-0.0439	0.6326	101.2013	136.864	58.3923
26	0.5131	0.122	-0.3364	0.1356	-0.0368	0.4434	-0.0451	0.3171	-0.1824	0.3962	0.3268	0.0796	0.1906	0.064	0.0009	0.4003	0.014	-0.0351	0.5136	-0.0833	0.5509	100.2101	144.1056	59.1876
27	0.088	-0.1546	0.0548	0.4163	0.0537	-0.0021	-0.3403	-0.3489	0.5923	0.7827	0.6014	-1.3423	-0.9128	0.748	-0.0257	0.7272	-0.0528	-0.0191	0.696	-0.116	0.9341	112.2358	167.7971	67.364
28	-0.0059	-0.0937	0.1202	0.5548	0.2476	0.1919	-0.0297	0.2367	0.0322	0.0391	0.057	0.2191	-0.0128	0.0516	0.0002	0.4446	0.0043	0.0073	0.5187	-0.0569	0.4902	95.7736	141.4362	58.8732
29	0.2492	-0.125	-0.2353	0.3405	-0.1281	0.2604	-0.0252	0.6055	0.2341	-0.4482	0.0108	-0.0108	-0.0649	-0.0359	0.0005	0.429	0.0008	-0.037	0.5725	0.0063	0.445	88.0668	142.9796	50.0748
30	0.2725	0.2635	-0.0335	0.7126	-0.0588	0.0807	0.116	-0.0876	0.185	0.177	-0.1548	0.6662	0.039	-0.0478	0.0003	0.4825	-0.016	-0.003	0.4664	0.0069	0.5243	84.222	157.8914	62.5161

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	CHAIN 'A' AND (RESID 2 THROUGH 42 )
2	X-RAY DIFFRACTION	2	CHAIN 'A' AND (RESID 43 THROUGH 54 )
3	X-RAY DIFFRACTION	3	CHAIN 'A' AND (RESID 55 THROUGH 72 )
4	X-RAY DIFFRACTION	4	CHAIN 'A' AND (RESID 73 THROUGH 97 )
5	X-RAY DIFFRACTION	5	CHAIN 'A' AND (RESID 98 THROUGH 112 )
6	X-RAY DIFFRACTION	6	CHAIN 'A' AND (RESID 113 THROUGH 129 )
7	X-RAY DIFFRACTION	7	CHAIN 'B' AND (RESID 1 THROUGH 33 )
8	X-RAY DIFFRACTION	8	CHAIN 'B' AND (RESID 34 THROUGH 42 )
9	X-RAY DIFFRACTION	9	CHAIN 'B' AND (RESID 43 THROUGH 65 )
10	X-RAY DIFFRACTION	10	CHAIN 'B' AND (RESID 66 THROUGH 129 )
11	X-RAY DIFFRACTION	11	CHAIN 'C' AND (RESID 1 THROUGH 42 )
12	X-RAY DIFFRACTION	12	CHAIN 'C' AND (RESID 43 THROUGH 54 )
13	X-RAY DIFFRACTION	13	CHAIN 'C' AND (RESID 55 THROUGH 77 )
14	X-RAY DIFFRACTION	14	CHAIN 'C' AND (RESID 78 THROUGH 97 )
15	X-RAY DIFFRACTION	15	CHAIN 'C' AND (RESID 98 THROUGH 112 )
16	X-RAY DIFFRACTION	16	CHAIN 'C' AND (RESID 113 THROUGH 129 )
17	X-RAY DIFFRACTION	17	CHAIN 'D' AND (RESID 1 THROUGH 33 )
18	X-RAY DIFFRACTION	18	CHAIN 'D' AND (RESID 34 THROUGH 42 )
19	X-RAY DIFFRACTION	19	CHAIN 'D' AND (RESID 43 THROUGH 54 )
20	X-RAY DIFFRACTION	20	CHAIN 'D' AND (RESID 55 THROUGH 76 )
21	X-RAY DIFFRACTION	21	CHAIN 'D' AND (RESID 77 THROUGH 97 )
22	X-RAY DIFFRACTION	22	CHAIN 'D' AND (RESID 98 THROUGH 129 )
23	X-RAY DIFFRACTION	23	CHAIN 'E' AND (RESID 1 THROUGH 10 )
24	X-RAY DIFFRACTION	24	CHAIN 'E' AND (RESID 11 THROUGH 42 )
25	X-RAY DIFFRACTION	25	CHAIN 'E' AND (RESID 43 THROUGH 54 )
26	X-RAY DIFFRACTION	26	CHAIN 'E' AND (RESID 55 THROUGH 65 )
27	X-RAY DIFFRACTION	27	CHAIN 'E' AND (RESID 66 THROUGH 82 )
28	X-RAY DIFFRACTION	28	CHAIN 'E' AND (RESID 83 THROUGH 97 )
29	X-RAY DIFFRACTION	29	CHAIN 'E' AND (RESID 98 THROUGH 112 )
30	X-RAY DIFFRACTION	30	CHAIN 'E' AND (RESID 113 THROUGH 129 )

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About Yorodumi

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Yorodumi